HowTo B

Neural Network Potential - Molecular Dynamics

October 31, 2024

Important Informations

Warning

Links to the Google Sheets with the assigned temperatures and hydrogen loadings:

Each student will be assigned two specific temperature values and two different hydrogen loadings for the simulations. One temperature will be used for Part B.1 and the other for Part B.2. The hydrogen loadings will be used for the simulations in Part B.1

Important

Before you run any simulations, please make sure you know your assigned TEMPERATURE values.

Tools and Programs

All tools and programs are provided by the Hofer Lab. The simulaton engine is PQ. The analysis tools are written in Python and C, and are partially based on the PQAnalysis library.

The required tools and programs for this exercise are provided by executing the following command:

module load pq

Important

This command needs to be executed only once per terminal session. If you close the terminal, you will need to execute the command again when you open a new terminal.

Tools and Programs

The simulation engine PQ can be executed by running the following command:

PQ <input_file>

The analysis tools are written in an intuitive way and have a help function that can be accessed by running the script with the --help flag. For example:

<analysis_tool> --help

Analysis Tools

The following analysis tools are provided for this exercise:

Tool	Description
`average_a`	Averages the lattice parameter a of the provided box files.
`average_V`	Averages the volume of the provided box files.
`extract_h2`	Extracts the hydrogen molecules of trajectory/velocity-files and calculates the center of mass coordinates/velocities.
`msd`	Calculates the mean squared displacement of the hydrogen molecules from a trajectory. (Note: The hydrogen molecules have to be extracted first using `extract_h2`).
`rdf`	Calculates the radial distribution function of the hydrogen molecule from a trajectory.
`vacf`	Calculates the velocity autocorrelation function of the hydrogen molecule from a velocity file. (Note: The hydrogen molecules have to be extracted first using `extract_h2`).
`linearfit`	Fits a linear function to the mean squared displacement data to calculate the diffusion coefficient according to the Einstein relation.
`integration`	Integrates the velocity autocorrelation function to calculate the diffusion coefficient according to the Green-Kubo relation.

Files

The folders /media/TC_Lehre/03_PR_Fortgeschrittene_Uebungen_zu_TC_und_Comp_Chemie/zif8-h2/zif8_files contains all necessary files for the simulations. The files are organized in the following way:

File Structure

├── general_input
│   ├── moldescriptor.dat
│   ├── run-01.in
│   ├── run-02.in
│   ├── run-03.in
│   └── run-04.in
├── h2
│   ├── h2.rst
│   └── shake_h2.top
└── preeq
    ├── 248
    │   ├── shake_zif8_248.top
    │   └── zif8_preeq_248.rst
    ├── 273
    │   ├── shake_zif8_273.top
    │   └── zif8_preeq_273.rst
    ├── 298
    │   ├── shake_zif8_298.top
    │   └── zif8_preeq_298.rst
    ├── 323
    │   ├── shake_zif8_323.top
    │   └── zif8_preeq_323.rst
    ├── 348
    │   ├── shake_zif8_348.top
    │   └── zif8_preeq_348.rst
    ├── 373
    │   ├── shake_zif8_373.top
    │   └── zif8_preeq_373.rst
    └── 398
        ├── shake_zif8_398.top
        └── zif8_preeq_398.rst

Files

The folders /media/TC_Lehre/03_PR_Fortgeschrittene_Uebungen_zu_TC_und_Comp_Chemie/zif8-h2/zif8_files contains all necessary files for the simulations. The files are organized in the following way:

Folder/File	Description
`general_input`	Contains the input files for the simulations (`moldescriptor.dat` and `run-0*.in`).
`h2`	Contains the hydrogen restart-file (`h2.rst`) and the topology file (`shake_h2.top`).
`preeq`	Contains the equilibration restart-files (`zif8_preeq_.rst`) and the topology files (`shake_zif8_.top`).

Part B.1) Gas simulation in ZIF-8

The first part of the exercise is to simulate the diffusion of hydrogen molecules in the ZIF-8 framework at the assigned temperature values. The hydrogen loading is set to the two assigned loadings per student.

Note

This part of the exercise is performed twice with the two assigned hydrogen loadings. The simulations can be run in parallel.

System Setup

The system setup is done by running the following command:

1. Copy the necessary files to the working directory

cp /media/TC_Lehre/03_PR_Fortgeschrittene_Uebungen_zu_TC_und_Comp_Chemie/zif8-h2/zif8_files/h2/* .
cp /media/TC_Lehre/03_PR_Fortgeschrittene_Uebungen_zu_TC_und_Comp_Chemie/zif8-h2/zif8_files/preeq/<TEMPERATURE>/* .
cp /media/TC_Lehre/03_PR_Fortgeschrittene_Uebungen_zu_TC_und_Comp_Chemie/zif8-h2/zif8_files/general_input/* .

2. Add the hydrogen loading to the topology and restart files (e.g. 32 hydrogen molecules and 298 K)

add_molecules zif8_preeq_298.rst h2.rst   \
  --rst-mol-desc-file moldescriptor.dat   \
  --top-file shake_zif8_298.top           \
  --added-top-file shake_h2.top           \
  --output-top-file shake.top             \
  -n 32                                   \
  > 32xh2-zif8-00.rst

Simulation

1. Edit the input file run-01.in to include your assigned temperature, generated restart file, and topology file.

...
# Temperature algorithm (velocity rescaling), Target T in K and Relaxation time in ps
      thermostat = velocity_rescaling; temp = XXX.XX; t_relaxation = 0.1;
...
# Files
      start_file    = XXX-00.rst;
      topology_file = XXX.top;

      file_prefix   = XXX-01;

Note

Replace XXX with the assigned temperature value and the corresponding restart and topology files. The file_prefix can be any name you choose. Please make sure to use -00.rst as the start file and -01 as the file prefix. This will help to keep track of the different simulation steps.

Simulation

2. Run NVT equlibration

PQ run-01.in

Important

The overall equilibration is split into two stages. The first stage is a 10 ps NVT equilibration (run-01.in). The second stage is a 10 ps NPT equilibration (run-02.in). After the equilibration, the production run is performed for 1 ns, which is split into 2 runs of 500 ps each (run-03.in and run-04.in).

Extract Hydrogen Molecule

Extract the hydrogen molecule from the trajectory and velocity files using the extract_h2 tool:

extract_h2 <trajectory_file>.xyz -n 276

and

extract_h2 <velocity_file>.vel -n 276

Note

The -n flag specifies the number of atoms of the empty ZIF-8 framework.

Einstein Relation

1. Calculate the mean squared displacement (MSD) of the hydrogen molecule using the msd tool:

msd

2. Fit a linear function to the MSD data using the linearfit tool:

linearfit --window 5

Important

For both assigned hydrogen loadings, insert the corresponding self-diffusion coefficient values into the Google Sheets.

Green-Kubo Relation

1. Calculate the velocity autocorrelation function (VACF) of the hydrogen molecule using the vacf tool:

vacf

2. Integrate the VACF data using the integration tool:

integration

Important

For both assigned hydrogen loadings, insert the corresponding self-diffusion coefficient values into the Google Sheets.

Part B.2) Thermal Expansion of ZIF-8

The second part of the exercise is to calculate the thermal expansion of the ZIF-8 framework at the assigned temperature values.

System Setup

The system setup is done by running the following command:

1. Copy the necessary files to the working directory

cp /media/TC_Lehre/03_PR_Fortgeschrittene_Uebungen_zu_TC_und_Comp_Chemie/zif8-h2/zif8_files/preeq/<TEMPERATURE>/* .
cp /media/TC_Lehre/03_PR_Fortgeschrittene_Uebungen_zu_TC_und_Comp_Chemie/zif8-h2/zif8_files/general_input/* .

Simulation

1. Edit the input file run-01.in to include your assigned temperature, generated restart file, and topology file.

...
# Temperature algorithm (velocity rescaling), Target T in K and Relaxation time in ps
      thermostat = velocity_rescaling; temp = XXX.XX; t_relaxation = 0.1;
...
# Files
      start_file    = zif8_preeq_XXX.rst;
      topology_file = shake_zif8_XXX.top;

      file_prefix   = zif8-01;

Note

Replace XXX with the assigned temperature value. The file_prefix can be any name you choose. Please make sure to use -01 as the file prefix. This will help to keep track of the different simulation steps.

Simulation

2. Run NVT equlibration

PQ run-01.in

Note

The overall equilibration is split into two stages. The first stage is a 10 ps NVT equilibration (run-01.in). The second stage is a 10 ps NPT equilibration (run-02.in). After the equilibration, the production run is performed for 500 ps (run-03.in). Only run run-03.in for the thermal expansion calculation.

Analysis

1. Average the lattice parameter a of the ZIF-8 framework using the average_a tool:

average_a zif8-03.box

2. Average the volume of the ZIF-8 framework using the average_V tool:

average_V zif8-03.box

3. Calculate the thermal expansion coefficient using the following formula, see thermal expansion